Metabolic profiling of the Arabidopsis pkl mutant reveals selective derepression of embryonic traits

Epigenetic modifications and miRNAs determine the transition of somatic cells into somatic embryos

KEY MESSAGE

This review discusses the epigenetic changes during somatic embryo (SE) development, highlights the genes and miRNAs involved in the transition of somatic cells into SEs as a result of epigenetic changes, and draws insights on biotechnological opportunities to study SE development. Somatic embryogenesis from somatic cells occurs in a series of steps. The transition of somatic cells into somatic embryos (SEs) is the most critical step under genetic and epigenetic regulations. Major regulatory genes such as SERK, WUS, BBM, FUS3/FUSA3, AGL15, and PKL, control SE steps and development by turning on and off other regulatory genes. Gene transcription profiles of somatic cells during SE development is the result of epigenetic changes, such as DNA and histone protein modifications, that control and decide the fate of SE formation. Depending on the type of somatic cells and the treatment with plant growth regulators, epigenetic changes take place dynamically. Either hypermethylation or hypomethylation of SE-related genes promotes the transition of somatic cells. For example, the reduced levels of DNA methylation of SERK and WUS promotes SE initiation. Histone modifications also promote SE induction by regulating SE-related genes in somatic cells. In addition, miRNAs contribute to the various stages of SE by regulating the expression of auxin signaling pathway genes (TIR1, AFB2, ARF6, and ARF8), transcription factors (CUC1 and CUC2), and growth-regulating factors (GRFs) involved in SE formation. These epigenetic and miRNA functions are unique and have the potential to regenerate bipolar structures from somatic cells when a pluripotent state is induced. However, an integrated overview of the key regulators involved in SE development and downstream processes is lacking. Therefore, this review discusses epigenetic modifications involved in SE development, SE-related genes and miRNAs associated with epigenetics, and common cis-regulatory elements in the promoters of SE-related genes. Finally, we highlight future biotechnological opportunities to alter epigenetic pathways using the genome editing tool and to study the transition mechanism of somatic cells.

Genes, proteins and other networks regulating somatic embryogenesis in plants

Background

Somatic embryogenesis (SE) is an intricate molecular and biochemical process principally based on cellular totipotency and a model in studying plant development. In this unique embryo-forming process, the vegetative cells acquire embryogenic competence under cellular stress conditions. The stress caused by plant growth regulators (PGRs), nutrient, oxygenic, or other signaling elements makes cellular reprogramming and transforms vegetative cells into embryos through activation/deactivation of a myriad of genes and transcriptional networks. Hundreds of genes have been directly linked to zygotic and somatic embryogeneses; some of them like SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE (SERK), LEAFY COTYLEDON (LEC), BABYBOOM (BBM), and AGAMOUS-LIKE 15 (AGL15) are very important and are part of molecular network.

Main text (observation)

This article reviews various genes/orthologs isolated from different plants; encoded proteins and their possible role in regulating somatic embryogenesis of plants have been discussed. The role of SERK in regulating embryogenesis is also summarized. Different SE-related proteins identified through LC–MS at various stages of embryogenesis are also described; a few proteins like 14-3-3, chitinase, and LEA are used as potential SE markers. These networks are interconnected in a complicated manner, posing challenges for their complete elucidation.

Conclusions

The various gene networks and factors controlling somatic embryogenesis have been discussed and presented. The roles of stress, PGRs, and other signaling elements have been discussed. In the last two-to-three decades’ progress, the challenges ahead and its future applications in various fields of research have been highlighted. The review also presents the need of high throughput, innovative techniques, and sensitive instruments in unraveling the mystery of SE.

Plant metabolic clusters - from genetics to genomics

Contents 771 I. 771 II. 772 III. 780 IV. 781 V. 786 786 References 786 SUMMARY: Plant natural products are of great value for agriculture, medicine and a wide range of other industrial applications. The discovery of new plant natural product pathways is currently being revolutionized by two key developments. First, breakthroughs in sequencing technology and reduced cost of sequencing are accelerating the ability to find enzymes and pathways for the biosynthesis of new natural products by identifying the underlying genes. Second, there are now multiple examples in which the genes encoding certain natural product pathways have been found to be grouped together in biosynthetic gene clusters within plant genomes. These advances are now making it possible to develop strategies for systematically mining multiple plant genomes for the discovery of new enzymes, pathways and chemistries. Increased knowledge of the features of plant metabolic gene clusters - architecture, regulation and assembly - will be instrumental in expediting natural product discovery. This review summarizes progress in this area.

Structure and function of histone methylation-binding proteins in plants

Post-translational modifications of histones play important roles in modulating many essential biological processes in both animals and plants. These covalent modifications, including methylation, acetylation, phosphorylation, ubiquitination, SUMOylation and so on, are laid out and erased by histone-modifying enzymes and read out by effector proteins. Recent studies have revealed that a number of developmental processes in plants are under the control of histone post-translational modifications, such as floral transition, seed germination, organogenesis and morphogenesis. Therefore, it is critical to identify those protein domains, which could specifically recognize these post-translational modifications to modulate chromatin structure and regulate gene expression. In the present review, we discuss the recent progress in understanding the structure and function of the histone methylation readers in plants, by focusing on Arabidopsis thaliana proteins.

CHD3 chromatin-remodeling factor PICKLE regulates floral transition partially via modulating LEAFY expression at the chromatin level in Arabidopsis

PICKLE (PKL), a putative CHD3 chromatin remodeling factor, has been suggested to be involved in multiple processes in Arabidopsis. Here, we confirmed the late-flowering phenotype caused by pkl mutation with pkl mutants in two different ecotypes, and investigated the possible mechanisms that account for PKL regulation of flowering time. Quantitative RT-PCR and RNA-seq assays showed that expression of the LEAFY gene (LFY) and a number of LFY-regulated floral homeotic genes were down-regulated in seedlings of the pkl mutants. As predicted, overexpression of LFY restored normal flowering time of pkl mutants. Our results suggest that PKL may be involved in regulating flowering time via LFY expression. To uncover the underlying mechanism, ChIP-PCR using anti-PKL was performed on materials from three developmental stages of seedlings. Our results showed that PKL associated with the genomic sequences of LFY, particularly at 10-day and 25-day after germination. We also showed that loss of PKL affected H3K27me3 level at the promoter of LFY. Taken together, our data suggest that transcriptional regulation of LFY at the chromatin level by PKL may at least partially account for the late-flowering phenotype of pkl mutants.

Roles and activities of chromatin remodeling ATPases in plants

Chromatin remodeling ATPases and their associated complexes can alter the accessibility of the genome in the context of chromatin by using energy derived from the hydrolysis of ATP to change the positioning, occupancy and composition of nucleosomes. In animals and plants, these remodelers have been implicated in diverse processes ranging from stem cell maintenance and differentiation to developmental phase transitions and stress responses. Detailed investigation of their roles in individual processes has suggested a higher level of selectivity of chromatin remodeling ATPase activity than previously anticipated, and diverse mechanisms have been uncovered that can contribute to the selectivity. This review summarizes recent advances in understanding the roles and activities of chromatin remodeling ATPases in plants.

Regulation of metabolic gene clusters in Arabidopsis thaliana

Recent discoveries have revealed that the genes for the biosynthesis of a variety of plant specialized metabolites are organized in operon-like clusters within plant genomes. Here we identify a regulatory process that is required for normal expression of metabolic gene clusters in Arabidopsis thaliana. Comparative gene expression analysis of a representative clustered gene was performed in a set of chromatin mutant lines. Subsequently, metabolite levels were analysed by GC-MS and the local chromatin structure was investigated by chromatin immunoprecipitation and nucleosome positioning. We show that the transcript levels of genes within two metabolic clusters are coordinately reduced in an arp6 and h2a.z background. We demonstrate that H2A.Z enrichment in the clusters is positively correlated with active cluster expression. We further show that nucleosome stability within the cluster regions is higher in the arp6 background compared with the wild-type. These results implicate ARP6 and H2A.Z in the regulation of metabolic clusters in Arabidopsis thaliana through localized chromatin modifications that enable the coordinate expression of groups of contiguous genes. These findings shed light on the complex process of cluster regulation, an area that could in the future open up new opportunities for the discovery and manipulation of specialized metabolic pathways in plants.

HISTONE DEACETYLASE19 interacts with HSL1 and participates in the repression of seed maturation genes in Arabidopsis seedlings

The seed maturation genes are specifically and highly expressed during late embryogenesis. In this work, yeast two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays revealed that HISTONE DEACETYLASE19 (HDA19) interacted with the HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE2-LIKE1 (HSL1), and the zinc-finger CW [conserved Cys (C) and Trp (W) residues] domain of HSL1 was responsible for the interaction. Furthermore, we found that mutations in HDA19 resulted in the ectopic expression of seed maturation genes in seedlings, which was associated with increased levels of gene activation marks, such as Histone H3 acetylation (H3ac), Histone H4 acetylation (H4ac), and Histone H3 Lys 4 tri-methylation (H3K4me3), but decreased levels of the gene repression mark Histone H3 Lys 27 tri-methylation (H3K27me3) in the promoter and/or coding regions. In addition, elevated transcription of certain seed maturation genes was also found in the hsl1 mutant seedlings, which was also accompanied by the enrichment of gene activation marks but decreased levels of the gene repression mark. Chromatin immunoprecipitation assays showed that HDA19 could directly bind to the chromatin of the seed maturation genes. These results suggest that HDA19 and HSL1 may act together to repress seed maturation gene expression during germination. Further genetic analyses revealed that the homozygous hsl1 hda19 double mutants are embryonic lethal, suggesting that HDA19 and HSL1 may play a vital role during embryogenesis.

Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana

The transcription factor LEAFY COTYLEDON1 (LEC1) controls aspects of early embryogenesis and seed maturation in Arabidopsis thaliana. To identify components of the LEC1 regulon, transgenic plants were derived in which LEC1 expression was inducible by dexamethasone treatment. The cotyledon-like leaves and swollen root tips developed by these plants contained seed-storage compounds and resemble the phenotypes produced by increased auxin levels. In agreement with this, LEC1 was found to mediate up-regulation of the auxin synthesis gene YUCCA10. Auxin accumulated primarily in the elongation zone at the root-hypocotyl junction (collet). This accumulation correlates with hypocotyl growth, which is either inhibited in LEC1-induced embryonic seedlings or stimulated in the LEC1-induced long-hypocotyl phenotype, therefore resembling etiolated seedlings. Chromatin immunoprecipitation analysis revealed a number of phytohormone- and elongation-related genes among the putative LEC1 target genes. LEC1 appears to be an integrator of various regulatory events, involving the transcription factor itself as well as light and hormone signalling, especially during somatic and early zygotic embryogenesis. Furthermore, the data suggest non-embryonic functions for LEC1 during post-germinative etiolation.

A novel HSI2 mutation in Arabidopsis affects the PHD-like domain and leads to derepression of seed-specific gene expression

Two related B3 domain transcriptional repressors, HSI2 (HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE2)/VAL1 (VP1/ABI3-LIKE1) and HSL1 (HSI2-LIKE1)/VAL2, function redundantly to repress key transcriptional regulators of seed maturation genes in Arabidopsis thaliana seedlings. Using a forward genetic screen designed to isolate trans-acting mutants that affected expression of a transgene containing the glutathione S-transferase F8 promoter::luciferase (GSTF8::LUC) reporter, we identified a novel HSI2 mutant allele, hsi2-4, that exhibits constitutively elevated luciferase expression while expression of the endogenous GSTF8 transcript remains unchanged. The hsi2-4 lesion was found to be a missense mutation that results in the substitution of a conserved cysteine within the plant homeodomain-like (PHD) motif of HSI2. Microarray analysis of hsi2-4 and hsi2-4 hsl1 mutants indicated that the HSI2 PHD-like domain functions non-redundantly to repress a subset of seed maturation genes, including those that encode AGL15 (AGAMOUS-LIKE15), FUSCA3 (FUS3), cruciferins, cupin family proteins, late-embryogenesis abundant protein, oleosins, 2S albumins and other seed-specific proteins in Arabidopsis seedlings. Many genes that are responsive to this mutation in the HSI2 PHD-like domain are enriched in histone H3 trimethylation on lysine 27 residues (H3K27me3), a repressive epigenetic mark. Chromatin immunoprecipitation analysis showed that sequences of the GSTF8::LUC transgene are enriched in H3K27me3 in a HSI2 PHD domain-dependent manner. These results indicate that the transcriptional repression activity of the HSI2 PHD domain could be mediated, at least in part, by its participation in the deposition of H3K27me3 on the chromatin of specific target genes.

The CHD3 remodeler PICKLE associates with genes enriched for trimethylation of histone H3 lysine 27

In Arabidopsis (Arabidopsis thaliana), the ATP-dependent chromatin remodeler PICKLE (PKL) determines expression of genes associated with developmental identity. PKL promotes the epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3) that facilitates repression of tissue-specific genes in plants. It has previously been proposed that PKL acts indirectly to promote H3K27me3 by promoting expression of the POLYCOMB REPRESSIVE COMPLEX2 complex that generates H3K27me3. We undertook expression and chromatin immunoprecipitation analyses to further characterize the contribution of PKL to gene expression and developmental identity. Our expression data support a critical and specific role for PKL in expression of H3K27me3-enriched loci but do not support a role for PKL in expression of POLYCOMB REPRESSIVE COMPLEX2. Moreover, our chromatin immunoprecipitation data reveal that PKL protein is present at the promoter region of multiple H3K27me3-enriched loci, indicating that PKL directly acts on these loci. In particular, we find that PKL is present at LEAFY COTYLEDON1 and LEAFY COTYLEDON2 during germination, which is when PKL acts to repress these master regulators of embryonic identity. Surprisingly, we also find that PKL is present at the promoters of actively transcribed genes that are ubiquitously expressed such as ACTIN7 and POLYUBIQUITIN10 that do not exhibit PKL-dependent expression. Taken together, our data contravene the previous model of PKL action and instead support a direct role for PKL in determining levels of H3K27me3 at repressed loci. Our data also raise the possibility that PKL facilitates a common chromatin remodeling process that is not restricted to H3K27me3-enriched regions.

MGOUN1 encodes an Arabidopsis type IB DNA topoisomerase required in stem cell regulation and to maintain developmentally regulated gene silencing

Maintenance of stem cells in the Arabidopsis thaliana shoot meristem is regulated by signals from the underlying cells of the organizing center, provided through the transcription factor WUSCHEL (WUS). Here, we report the isolation of several independent mutants of MGOUN1 (MGO1) as genetic suppressors of ectopic WUS activity and enhancers of stem cell defects in hypomorphic wus alleles. mgo1 mutants have previously been reported to result in a delayed progression of meristem cells into differentiating organ primordia (Laufs et al., 1998). Genetic analyses indicate that MGO1 functions together with WUS in stem cell maintenance at all stages of shoot and floral meristems. Synergistic interactions of mgo1 with several chromatin mutants suggest that MGO1 affects gene expression together with chromatin remodeling pathways. In addition, the expression states of developmentally regulated genes are randomly switched in mgo1 in a mitotically inheritable way, indicating that MGO1 stabilizes epigenetic states against stochastically occurring changes. Positional cloning revealed that MGO1 encodes a putative type IB topoisomerase, which in animals and yeast has been shown to be required for regulation of DNA coiling during transcription and replication. The specific developmental defects in mgo1 mutants link topoisomerase IB function in Arabidopsis to stable propagation of developmentally regulated gene expression.

Molecular aspects of somatic-to-embryogenic transition in plants

Somatic embryogenesis (SE) is a model system for understanding the physiological, biochemical, and molecular biological events occurring during plant embryo development. Plant somatic cells have the ability to undergo sustained divisions and give rise to an entire organism. This remarkable feature is called plant cell totipotency. SE is a notable illustration of plant totipotency and involves reprogramming of development in somatic cells toward the embryogenic pathway. Plant growth regularities, especially auxins, are key components as their exogenous application recapitulates the embryogenic potential of the mitotically quiescent somatic cells. It has been observed that there are genetic and also physiological factors that trigger in vitro embryogenesis in various types of plant somatic cells. Analysis of the proteome and transcriptome has led to the identification and characterization of certain genes involved in SE. Most of these genes, however, are upregulated only in the late developmental stages, suggesting that they do not play a direct role in the vegetative-to-embryogenic transition. However, the molecular bases of those triggering factors and the genetic and biochemical mechanisms leading to in vitro embryogenesis are still unknown. Here, we describe the plant factors that participate in the vegetative-to-embryogenic transition and discuss their possible roles in this process.

Increasing the flow of carbon into seed oil

The demand for vegetable oils for food, fuel (bio-diesel) and bio-product applications is increasing rapidly. In Canada alone, it is estimated that a 50 to 75% increase in canola oil production will be required to meet the demand for seed oil in the next 7-10years. Plant breeding and genetics have demonstrated that seed oil content is a quantitative trait based on a number of contributing factors including embryo genetic effects, cytoplasmic effects, maternal genetic effects, and genotype-environment interactions. Despite the involvement of numerous quantitative trait loci in determining seed oil content, genetic engineering to over-express/repress specific genes encoding enzymes and other proteins involved in the flow of carbon into seed oil has led to the development of transgenic lines with significant increases in seed oil content. Proteins encoded by these genes include enzymes catalyzing the production of building blocks for oil assembly, enzymes involved in oil assembly, enzymes regulating metabolic carbon partitioning between oil, carbohydrate and secondary metabolite fractions, and transcription factors which orchestrate metabolism at a more general level.

An epigenetic perspective on developmental regulation of seed genes

The developmental program of seeds is promoted by master regulators that are expressed in a seed-specific manner. Ectopic expression studies reveal that expression of these master regulators and other transcriptional regulators is sufficient to promote seed-associated traits, including generation of somatic embryos. Recent work highlights the importance of chromatin-associated factors in restricting expression of seed-specific genes, in particular PcG proteins and ATP-dependent remodelers. This review summarizes what is known regarding factors that promote zygotic and/or somatic embryogenesis and the chromatin machinery that represses their expression. Characterization of the regulation of seed-specific genes reveals that plant chromatin-based repression systems exhibit broad conservation with and surprising differences from animal repression systems.

Repression of seed maturation genes by a trihelix transcriptional repressor in Arabidopsis seedlings

The seed maturation program is repressed during germination and seedling development so that embryonic genes are not expressed in vegetative organs. Here, we describe a regulator that represses the expression of embryonic seed maturation genes in vegetative tissues. ASIL1 (for Arabidopsis 6b-interacting protein 1-like 1) was isolated by its interaction with the Arabidopsis thaliana 2S3 promoter. ASIL1 possesses domains conserved in the plant-specific trihelix family of DNA binding proteins and belongs to a subfamily of 6b-interacting protein 1-like factors. The seedlings of asil1 mutants exhibited a global shift in gene expression to a profile resembling late embryogenesis. LEAFY COTYLEDON1 and 2 were markedly derepressed during early germination, as was a large subset of seed maturation genes, such as those encoding seed storage proteins and oleosins, in seedlings of asil1 mutants. Consistent with this, asil1 seedlings accumulated 2S albumin and oil with a fatty acid composition similar to that of seed-derived lipid. Moreover, ASIL1 specifically recognized a GT element that overlaps the G-box and is in close proximity to the RY repeats of the 2S promoters. We suggest that ASIL1 targets GT-box-containing embryonic genes by competing with the binding of transcriptional activators to this promoter region.

The Arabidopsis BRAHMA chromatin-remodeling ATPase is involved in repression of seed maturation genes in leaves

Synthesis and accumulation of seed storage proteins (SSPs) is an important aspect of the seed maturation program. Genes encoding SSPs are specifically and highly expressed in the seed during maturation. However, the mechanisms that repress the expression of these genes in leaf tissue are not well understood. To gain insight into the repression mechanisms, we performed a genetic screen for mutants that express SSPs in leaves. Here, we show that mutations affecting BRAHMA (BRM), a SNF2 chromatin-remodeling ATPase, cause ectopic expression of a subset of SSPs and other embryogenesis-related genes in leaf tissue. Consistent with the notion that such SNF2-like ATPases form protein complexes in vivo, we observed similar phenotypes for mutations of AtSWI3C, a BRM-interacting partner, and BSH, a SNF5 homolog and essential SWI/SNF subunit. Chromatin immunoprecipitation experiments show that BRM is recruited to the promoters of a number of embryogenesis genes in wild-type leaves, including the 2S genes, expressed in brm leaves. Consistent with its role in nucleosome remodeling, BRM appears to affect the chromatin structure of the At2S2 promoter. Thus, the BRM-containing chromatin-remodeling ATPase complex involved in many aspects of plant development mediates the repression of SSPs in leaf tissue.

The CHD3 remodeler PICKLE promotes trimethylation of histone H3 lysine 27

CHD3 proteins are ATP-dependent chromatin remodelers that contribute to repression of developmentally regulated genes in both animal and plant systems. In animals, this repression has been linked to a multiple subunit complex, Mi-2/NuRD, whose constituents include a CHD3 protein, a histone deacetylase, and a methyl-CpG-binding domain protein. In Arabidopsis, PICKLE (PKL) codes for a CHD3 protein that acts during germination to repress expression of seed-associated genes. Repression of seed-associated traits is promoted in pkl seedlings by the plant growth regulator gibberellin (GA). We undertook a microarray analysis to determine how PKL and GA act to promote the transition from seed to seedling. We found that PKL and GA act in separate pathways to repress expression of seed-specific genes. Comparison of genomic datasets revealed that PKL-dependent genes are enriched for trimethylation of histone H3 lysine 27 (H3K27me3), a repressive epigenetic mark. Chromatin immunoprecipitation studies demonstrate that PKL promotes H3K27me3 in both germinating seedlings and in adult plants but do not identify a connection between PKL-dependent expression and acetylation levels. Taken together, our analyses illuminate a new pathway by which CHD3 remodelers contribute to repression in eukaryotes.

Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis

Seeds represent the main source of nutrients for animals and humans, and knowledge of their biology provides tools for improving agricultural practices and managing genetic resources. There is also tremendous interest in using seeds as a sustainable alternative to fossil reserves for green chemistry. Seeds accumulate large amounts of storage compounds such as carbohydrates, proteins and oils. It would be useful for agro-industrial purposes to produce seeds that accumulate these storage compounds more specifically and at higher levels. The main metabolic pathways necessary for oil, starch or protein accumulation are well characterized. However, the overall regulation of partitioning between the various pathways remains unclear. Such knowledge could provide new molecular tools for improving the qualities of crop seeds (Focks and Benning, 1998, Plant Physiol. 118, 91). Studies to improve understanding of the genetic controls of seed development and metabolism therefore remain a key area of research. In the model plant Arabidopsis, genetic analyses have demonstrated that LEAFY COTYLEDON genes, namely LEC1, LEC2 and FUSCA3 (FUS3), are key transcriptional regulators of seed maturation, together with ABSCISIC ACID INSENSITIVE 3 (ABI3). Interestingly, LEC2, FUS3 and ABI3 are related proteins that all contain a 'B3' DNA-binding domain. In recent years, genetic and molecular studies have shed new light on the intricate regulatory network involving these regulators and their interactions with other factors such as LEC1, PICKLE, ABI5 or WRI1, as well as with sugar and hormonal signaling. Here, we summarize the most recent advances in our understanding of this complex regulatory network and its role in the control of seed maturation.

The role of chromatin-remodeling factor PKL in balancing osmotic stress responses during Arabidopsis seed germination

Embryogenesis in Arabidopsis results in mature, osmotolerant embryos within dry seeds. Late-embryogenesis programs involve the transcription factors ABI3 and ABI5, which are necessary for osmotolerance. ABI3 and ABI5 are degraded in seeds initiating germination, abolishing their protected state. However, during an early stage of germination, strong osmotic stresses, or ABA exposure maintain ABI3 and ABI5 expression, leading to growth arrest, and osmotolerance. Mild stress stimuli delay ABI3 and ABI5 disappearance, retarding germination but not preventing eventual closure of embryogenesis programs. PICKLE (PKL), a putative chromatin modifier, is necessary to repress ABI3 and ABI5 expression during germination in response to ABA. We show that pkl mutants display persistent high expression of ABI3 and ABI5 upon ABA stimulation. In turn, maintenance of ABI5 expression leads to hypersensitive germination responses to ABA in pkl seeds. We provide evidence that ABI3 and ABI5 are less associated with repressed chromatin in pkl mutants. Our results provide evidence that PKL-dependent repression of embryonic gene expression extends to late-embryogenesis genes and is associated with changes in chromatin. We suggest that effective closure of embryogenesis omostolerance programs during germination prevents excessive plant reactions to stress.

Metabolite profiling of Douglas-fir (Pseudotsuga menziesii) field trials reveals strong environmental and weak genetic variation

The primary objective of this study was to assess metabolomics for its capacity to discern biological variation among 10 full-sib families of a Douglas-fir tree breeding population, replicated on two sites. The differential accumulation of small metabolites in developing xylem was examined through metabolite profiles (139 metabolites common to 181 individual trees) generated by gas chromatography mass spectrometry and a series of statistical analyses that incorporated family, site, and tree growth and quantitative phenotypic wood traits (wood density, microfibril angle, wood chemistry and fiber morphology). Multivariate discriminant, canonical discriminant and factor analyses and broad-sense heritabilities revealed that metabolic and phenotypic traits alike were strongly related to site, while similar associations relating to genetic (family) structure were weak in comparison. Canonical correlation analysis subsequently identified correlations between specific phenotypic traits (i.e. tree growth, fibre morphology and wood chemistry) and metabolic traits (i.e. carbohydrate and lignin biosynthetic metabolites), demonstrating a coherent relationship between genetics, metabolism, environmental and phenotypic expression in wood-forming tissue. The association between cambial metabolites and tree phenotype, as revealed by metabolite profiling, demonstrates the value of metabolomics for systems biology approaches to understanding tree growth and secondary cell wall biosynthesis in plants.

PICKLE acts during germination to repress expression of embryonic traits

PICKLE (PKL) codes for a CHD3 chromatin remodeling factor that plays multiple roles in Arabidopsis growth and development. Previous analysis of the expression of genes that exhibit PKL-dependent regulation suggested that PKL acts during germination to repress expression of embryonic traits. In this study, we examined the expression of PKL protein to investigate when and where PKL acts to regulate development. A PKL:eGFP translational fusion is preferentially localized in the nucleus of cells, consistent with the proposed role for PKL as a chromatin remodeling factor. A steroid-inducible version of PKL [a fusion of PKL to the glucocorticoid receptor (PKL:GR)] was used to examine when PKL acts to repress expression of embryonic traits. We found that activation of PKL:GR during germination was sufficient to repress expression of embryonic traits in the primary roots of pkl seedlings, whereas activation of PKL:GR after germination had little effect. In contrast, we observed that PKL is required continuously after germination to repress expression of PHERES1, a type I MADS box gene that is normally expressed during early embryogenesis in wild-type plants. Thus, PKL acts at multiple points during development to regulate patterns of gene expression in Arabidopsis.

Gibberellin metabolism and signaling

Gibberellins (GAs) are a family of plant hormones controlling many aspects of plant growth and development including stem elongation, germination, and the transition from vegetative growth to flowering. Cloning of the genes encoding GA biosynthetic and inactivating enzymes has led to numerous insights into the developmental regulation of GA hormone accumulation that is subject to both positive and negative feedback regulation. Genetic and biochemical analysis of GA-signaling genes has revealed that posttranslational regulation of DELLA protein accumulation is a key control point in GA response. The highly conserved DELLA proteins are a family of negative regulators of GA signaling that appear subject to GA-stimulated degradation through the ubiquitin-26S proteasome pathway. This review discusses the regulation of GA hormone accumulation and signaling in the context of its role in plant growth and development.

ATP-dependent chromatin remodeling

The study of chromatin and how this dynamic structure modulates events in the eukaryotic nucleus has become an increasingly important topic in biomedical research. A large number of enzymes have been discovered that are responsible for modifying and altering chromatin structure, either globally or specifically at particular gene promoters or regions of the chromosome. This chapter provides an introduction to the structure of chromatin and then describes how special classes of enzymes modulate chromatin structure to allow access to DNA.